Photoshop CS6: Line tool prints arrow instead of line
This thing has been giving me a headache too! I finally found the answer myself.
Do you see the arrow drop-down menu next to the Custom Shape tool? There is a check box for Start and End. Uncheck them both, and it will draw a line instead of an arrow!
If you're looking for the arrowhead options, it's located on the gear (default position):
If that doesn't work, try to reset the line tool: